Read PURPLE CNV Gene File

Reads the purple.cnv.gene.tsv file, which summarises copy number alterations of each gene in the HMF panel (see this table).

Usage

purple_cnv_som_gene_read(x)

Arguments

x

Path to purple.cnv.gene.tsv file.

Value

The input file as a tibble.

Examples

x <- system.file("extdata/purple/purple.cnv.gene.tsv", package = "gpgr")
(p <- purple_cnv_som_gene_read(x))
#> # A tibble: 230 × 18
#>    chromosome  start    end gene      minCopyNumber maxCopyNumber somaticRegions
#>    <chr>       <int>  <int> <chr>             <dbl>         <dbl>          <dbl>
#>  1 chr1        11869  14409 DDX11L1            1.96          1.96              1
#>  2 chr1        14404  29570 WASH7P             1.96          1.96              1
#>  3 chr1        17369  17436 MIR6859-1          1.96          1.96              1
#>  4 chr1        29554  31109 MIR1302-…          1.96          1.96              1
#>  5 chr1        30366  30503 MIR1302-2          1.96          1.96              1
#>  6 chr1        34554  36081 FAM138A            1.96          1.96              1
#>  7 chr1        52473  53312 OR4G4P             1.96          1.96              1
#>  8 chr1        57598  64116 OR4G11P            1.96          1.96              1
#>  9 chr1        65419  71585 OR4F5              1.96          1.96              1
#> 10 chr1       131025 134836 CICP27             1.96          1.96              1
#> # ℹ 220 more rows
#> # ℹ 11 more variables: transcriptId <chr>, isCanonical <chr>,
#> #   chromosomeBand <chr>, minRegions <dbl>, minRegionStart <int>,
#> #   minRegionEnd <int>, minRegionStartSupport <chr>, minRegionEndSupport <chr>,
#> #   minRegionMethod <chr>, minMinorAlleleCopyNumber <dbl>,
#> #   depthWindowCount <int>